Parliament2: Accurate structural variant calling at scale.
Parliament2: Accurate structural variant calling at scale.
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DOI：
10.1093/gigascience/giaa145
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发表时间：
2020-12-21
期刊：
影响因子：
9.2
通讯作者：
Sedlazeck FJ
中科院分区：
文献类型：
--
作者：
Zarate S;Carroll A;Mahmoud M;Krasheninina O;Jun G;Salerno WJ;Schatz MC;Boerwinkle E;Gibbs RA;Sedlazeck FJ
结构变异（SV）是遗传多样性和基因组疾病的关键因素。为了预测SV的表型影响，需要更好地估计SV的发生率和频率，最好是来自大型的种族多样性队列。因此，目前的标准方法需要使用短的双端读段，这对于检测来说仍然具有挑战性，特别是在数百至数千个样品的规模下。我们提出了一个共识SV框架，它利用多种同类最佳方法从大规模的短读段DNA序列数据中识别高质量的SV。Question2集成了预安装的SV调用程序，这些调用程序针对并行高效执行进行了优化，以减少总体运行时间和成本。我们证明了当应用于来自NovaSeq和HiSeq X平台的数据时，在所有大小类别中使用瓶内基因组（GIAB）SV调用集的准确性。报告的每个SV的质量评分在不同SV类型和尺寸类别之间进行校准。在GIAB的独立金标准中，B2具有最高的F1得分（74.27%）。我们通过在GRCH 38上处理所有1000个基因组样本（2，691个样本）来说明计算性能。Docent2提高了单个方法的运行时性能，并且是开源的（https：//github.com/slzarate/docent2），并且提供了Docker镜像和WDL实现。Quient2提供了来自短读段DNA序列数据的高度准确的单样本SV调用集，并在云或集群环境中实现了具有成本效益的应用程序，可处理数千个样本。
Structural variants (SVs) are critical contributors to genetic diversity and genomic disease. To predict the phenotypic impact of SVs, there is a need for better estimates of both the occurrence and frequency of SVs, preferably from large, ethnically diverse cohorts. Thus, the current standard approach requires the use of short paired-end reads, which remain challenging to detect, especially at the scale of hundreds to thousands of samples. We present Parliament2, a consensus SV framework that leverages multiple best-in-class methods to identify high-quality SVs from short-read DNA sequence data at scale. Parliament2 incorporates pre-installed SV callers that are optimized for efficient execution in parallel to reduce the overall runtime and costs. We demonstrate the accuracy of Parliament2 when applied to data from NovaSeq and HiSeq X platforms with the Genome in a Bottle (GIAB) SV call set across all size classes. The reported quality score per SV is calibrated across different SV types and size classes. Parliament2 has the highest F1 score (74.27%) measured across the independent gold standard from GIAB. We illustrate the compute performance by processing all 1000 Genomes samples (2,691 samples) in <1 day on GRCH38. Parliament2 improves the runtime performance of individual methods and is open source (https://github.com/slzarate/parliament2), and a Docker image, as well as a WDL implementation, is available. Parliament2 provides both a highly accurate single-sample SV call set from short-read DNA sequence data and enables cost-efficient application over cloud or cluster environments, processing thousands of samples.
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影响因子：
64.8
作者：
Sudmant PH;Rausch T;Gardner EJ;Handsaker RE;Abyzov A;Huddleston J;Zhang Y;Ye K;Jun G;Fritz MH;Konkel MK;Malhotra A;Stütz AM;Shi X;Casale FP;Chen J;Hormozdiari F;Dayama G;Chen K;Malig M;Chaisson MJP;Walter K;Meiers S;Kashin S;Garrison E;Auton A;Lam HYK;Mu XJ;Alkan C;Antaki D;Bae T;Cerveira E;Chines P;Chong Z;Clarke L;Dal E;Ding L;Emery S;Fan X;Gujral M;Kahveci F;Kidd JM;Kong Y;Lameijer EW;McCarthy S;Flicek P;Gibbs RA;Marth G;Mason CE;Menelaou A;Muzny DM;Nelson BJ;Noor A;Parrish NF;Pendleton M;Quitadamo A;Raeder B;Schadt EE;Romanovitch M;Schlattl A;Sebra R;Shabalin AA;Untergasser A;Walker JA;Wang M;Yu F;Zhang C;Zhang J;Zheng-Bradley X;Zhou W;Zichner T;Sebat J;Batzer MA;McCarroll SA;1000 Genomes Project Consortium;Mills RE;Gerstein MB;Bashir A;Stegle O;Devine SE;Lee C;Eichler EE;Korbel JO
通讯作者：
Korbel JO
影响因子：
48
作者：
Sedlazeck FJ;Rescheneder P;Smolka M;Fang H;Nattestad M;von Haeseler A;Schatz MC
通讯作者：
Schatz MC
影响因子：
46.9
作者：
Zook JM;Hansen NF;Olson ND;Chapman L;Mullikin JC;Xiao C;Sherry S;Koren S;Phillippy AM;Boutros PC;Sahraeian SME;Huang V;Rouette A;Alexander N;Mason CE;Hajirasouliha I;Ricketts C;Lee J;Tearle R;Fiddes IT;Barrio AM;Wala J;Carroll A;Ghaffari N;Rodriguez OL;Bashir A;Jackman S;Farrell JJ;Wenger AM;Alkan C;Soylev A;Schatz MC;Garg S;Church G;Marschall T;Chen K;Fan X;English AC;Rosenfeld JA;Zhou W;Mills RE;Sage JM;Davis JR;Kaiser MD;Oliver JS;Catalano AP;Chaisson MJP;Spies N;Sedlazeck FJ;Salit M
通讯作者：
Salit M
DOI：
10.1093/bioinformatics/bts378
发表时间：
2012-09-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Rausch T;Zichner T;Schlattl A;Stütz AM;Benes V;Korbel JO
通讯作者：
Korbel JO
影响因子：
48
作者：
Wang, Jianmin;Mullighan, Charles G.;Easton, John;Roberts, Stefan;Heatley, Sue L.;Ma, Jing;Rusch, Michael C.;Chen, Ken;Harris, Christopher C.;Ding, Li;Holmfeldt, Linda;Payne-Turner, Debbie;Fan, Xian;Wei, Lei;Zhao, David;Obenauer, John C.;Naeve, Clayton;Mardis, Elaine R.;Wilson, Richard K.;Downing, James R.;Zhang, Jinghui
通讯作者：
Zhang, Jinghui